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01.
arXiv (math.PR) 2026-06-19

Theory of uncertain probability: can we derive the probability density function of uncertain random experiments with continuously changing conditions?

作者:

arXiv:2606.20169v1 Announce Type: new Abstract: This paper aims to explore the formation mechanism of probability distribution in situations where the differences among random experiments are distinguishable, and these differences continue to evolve along with the dynamic changes in conditions and their mechanisms of action. To this end, we are motivated to devise a new theoretical system – theory of uncertain probability (TUP) with Kolmogorov's system and nonlinear theories as special cases. TUP develops a novel model that integrates probability and uncertainty as well as the known and unknown to more accurately depict numerous typical random phenomena under more realistic assumptions, and thus provides appropriate tools for greater variety of real needs. It also allows for pioneering interpretation of the causal mechanisms underlying many important distributional characteristics and incorporation of pathwise property to distribution model.

02.
arXiv (CS.CV) 2026-06-18

Beyond Nearest Neighbor Interpolation in Data Augmentation

Avoiding the risk of undefined categorical labels using nearest neighbor interpolation overlooks the risk of exacerbating pixel level annotation errors in augmented training data. Additionally, the inherent low pass filtering effects of interpolation algorithms exacerbate the risk of degrading high frequency structural details within annotated regions of interest. To avoid these risks, the author modified convolutional neural networks data transformation functions by incorporating a modified geometric transformation function, removing reliance on nearest neighbor interpolation, and integrating a mean-based class filtering mechanism to handle undefined categorical labels with alternative interpolation algorithms. The author also implemented an offline data augmentation pipeline to generate interpolation specific augmented training data, enabling quantitative assessment of interpolation specific low pass filtering effects on augmented training data. Experimental evaluation on three medical image segmentation datasets and the XBAT+ datasets demonstrated performance gains across multiple quantitative metrics.

03.
arXiv (CS.CL) 2026-06-16

Evaluating and Preserving Lexical Stress in English-to-Chinese Speech-to-Speech Translation

Speech-to-speech translation (S2ST) systems have achieved impressive progress in semantic accuracy and speech naturalness. However, the cross-lingual transfer of lexical stress, a vital cue for emphasis and speaker intent, remains heavily underexplored, compounded by a lack of reliable automatic evaluation metrics for tonal languages like Chinese. We investigate English-to-Chinese S2ST stress transfer by constructing a stress-annotated Chinese dataset and an XLS-R-based Mandarin stress detector. Integrating this with the English EmphAssess system, we propose a novel objective metric for cross-lingual stress evaluation. Furthermore, we fine-tune CosyVoice3 to build a stress-aware S2ST system. Experiments demonstrate that our proposed S2ST architecture significantly outperforms existing systems in stress translation capability while maintaining competitive translation quality. Furthermore, our evaluation metric exhibits a strong correlation with human subjective judgments.

05.
arXiv (CS.CV) 2026-06-17

Revisiting Structural Dependency in Autoregressive Multi-Task Table Recognition via Order-Independent Cell-Level Representations

Multi-task table recognition jointly addresses table structure prediction, cell localization, and cell content recognition within a unified framework. Existing approaches often rely on autoregressive decoders to generate table structures and reuse their hidden states for cell localization and content recognition. This autoregressive generation process can make cell representations order-dependent, degrading global consistency across cells. This paper proposes a structural refinement module that produces order-independent cell features through non-causal attention. This design enables parallel inference of cell contents while conditioning each cell on global context encoded in the refined features. Experiments on two large datasets demonstrate consistent gains in cell localization and end-to-end recognition, while reducing overall inference time by around threefold.

06.
arXiv (CS.CV) 2026-06-16

Power Battery Detection

Power batteries are essential components in electric vehicles, where internal structural defects can pose serious safety risks. We conduct a comprehensive study on a new task, power battery detection (PBD), which aims to localize the dense endpoints of cathode and anode plates from industrial X-ray images for quality inspection. Manual inspection is inefficient and error-prone, while traditional vision algorithms struggle with densely packed plates, low contrast, scale variation, and imaging artifacts. To address this issue and drive more attention into this meaningful task, we present PBD5K, the first large-scale benchmark for this task, consisting of 5,000 X-ray images from nine battery types with fine-grained annotations and eight types of real-world visual interference. To support scalable and consistent labeling, we develop an intelligent annotation pipeline that combines image filtering, model-assisted pre-labeling, cross-verification, and layered quality evaluation. We formulate PBD as a point-level segmentation problem and propose MDCNeXt, a model designed to extract and integrate multi-dimensional structure clues including point, line, and count information from the plate itself. To improve discrimination between plates and suppress visual interference, MDCNeXt incorporates two state space modules. The first is a prompt-filtered module that learns contrastive relationships guided by task-specific prompts. The second is a density-aware reordering module that refines segmentation in regions with high plate density. In addition, we propose a distance-adaptive mask generation strategy to provide robust supervision under varying spatial distributions of anode and cathode positions. The source code and datasets will be publicly available at \href{https://github.com/Xiaoqi-Zhao-DLUT/X-ray-PBD}{PBD5K}.

07.
arXiv (CS.LG) 2026-06-18

Identifying Structural Biases from Causal Mechanism Shifts

arXiv:2606.18834v1 Announce Type: new Abstract: Causal discovery methods commonly assume that all data is independently and identically distributed (i.i.d.) and that there are no unmeasured variables affecting the system. In practice, these assumptions are often violated, leading to inaccurate inference. In this paper, we study how to identify hidden confounding and selection biases from causal mechanism shifts. In particular, we show that structural biases lead to dependent mechanism shifts. That is, by considering for which variables the mechanisms change given data from different environments, we can tell which variables are unbiased, which are subject to hidden confounding, and which are undergoing selection bias. We formalize this into an empirically testable criterion based on mutual information, and show under which conditions it identifies structural biases. To tell which nodes are subject to what kind of bias, we introduce the StruBI algorithm. Experiments on synthetic and real-world data show that StruBI works well in practice, accurately recovering affected variable sets and types of biases, outperforming the state-of-the-art by a wide margin.

08.
arXiv (quant-ph) 2026-06-16

Orbital-optimized spin-adapted multistate contracted VQE for excited states and properties on quantum hardware

arXiv:2606.15489v1 Announce Type: new Abstract: We introduce the orbital-optimized multistate contracted variational quantum eigensolver (oo-MC-VQE) method with spin-adapted operators for the computation of ground and excited states, as well as state-specific and transition properties. The use of spin-adapted operators ensures that the spin symmetry of the reference states is conserved throughout the VQE optimization. In multistate variational approaches, achieving a balanced description of an increasing number of electronic states places growing demands on the expressibility of the underlying ansatz, thereby introducing a fundamental trade-off between accuracy and circuit complexity. We consider the effects of this trade-off explicitly and find that the number of circuit parameters required to obtain accurate results is reported to scale approximately linearly in the number of states. We further present an explicit quantum-circuit implementation of the oo-MC-VQE method and demonstrate its integration with quantum error mitigation techniques. Finally, we execute the method on real quantum devices to compute absorption spectra for two benchmark molecular systems.

09.
arXiv (quant-ph) 2026-06-19

Topological Quantum Interferometry

arXiv:2606.19730v1 Announce Type: new Abstract: Structured light provides high-dimensional Hilbert spaces holding tremendous potential for fundamental quantum optics and quantum technologies. However, existing characterization methods, like Hong-Ou-Mandel (HOM) interference, typically assume perfectly tuned conditions, overlooking the geometric physics governing spatial mode evolution. Here, we establish topological quantum interferometry driven by an interaction-based geometric phase, the exchange Berry phase (BPX). Our formalism generalizes $q$-plate state generation and characterization to arbitrary topological charges and (de)tuning conditions, demonstrating that BPX acts as a geometric marker governing spatial interference. We show BPX serves as a deterministic control parameter, decomposing two-photon spatial patterns into geometry-dictated fundamental modes. This mapping reveals topological invariants and phase singularities that function as a non-tomographic witness for state dimensionality estimation, circumventing full-state reconstruction. Being device-independent and highly scalable, this approach enables scalable high-dimensional characterization and topologically protected state selection, with direct applicability to quantum metrology and high-capacity quantum networks.

10.
arXiv (quant-ph) 2026-06-16

Adaptively secure unitary designs with constant non-Clifford cost

arXiv:2510.08129v2 Announce Type: replace Abstract: Randomness is a fundamental resource in quantum information, with crucial applications in cryptography, algorithms, and error correction. A central challenge is to construct unitary $k$-designs that closely approximate Haar-random unitaries while minimizing the costly use of non-Clifford operations. In this work, we present a protocol able to generate unitary $k$-designs on $n$ qubits, secure against any adversarial quantum measurement, with a system-size-independent number of non-Clifford gates. Our construction applies a $k$-design only to a subsystem of size $\Theta(k)$, independent of $n$. This ``seed'' design is then ``diluted'' across the entire $n$-qubit system by sandwiching it between two random Clifford operators. The resulting ensemble forms an $\varepsilon$-approximate unitary $k$-design on $n$ qubits. We prove that this construction achieves full quantum security against adaptive adversaries using only $\tilde{O}(k^2 \log\varepsilon^{-1})$ non-Clifford gates. If one requires security only against polynomial-time adaptive adversaries, the non-Clifford cost decreases to $\tilde{O}(k + \log^{1+c} \varepsilon^{-1})$. This is optimal, since we show that at least $\Omega(k)$ non-Clifford gates are required in this setting. Compared to existing approaches, our method significantly reduces non-Clifford overhead while strengthening security guarantees to adaptive security as well as removing artificial assumptions between $n$ and $k$. These results make high-order unitary designs practically attainable in near-term fault-tolerant quantum architectures.

11.
arXiv (CS.CV) 2026-06-12

Self-Evolving Vision-Language Models for Image Quality Assessment via Voting and Ranking

Improving vision-language models (VLMs) in the post-training stage typically relies on supervised fine-tuning or reinforcement learning, methods that necessitate costly, human-annotated data. While self-supervised techniques have proven effective for enhancing reasoning capabilities, their application to perceptual domains such as image quality assessment (IQA) remains largely unexplored. In this work, we introduce EvoQuality, a novel framework that enables a VLM to autonomously refine its quality perception capabilities without any ground-truth labels. EvoQuality adapts the principle of self-consistency to the ranking-based nature of IQA. It generates pseudo-labels by performing pairwise majority voting on the VLM's own outputs to establish a consensus on relative quality. These pseudo-rankings are then formulated into a fidelity reward that guides the model's iterative evolution through group relative policy optimization (GRPO). By iteratively leveraging its own predictions, EvoQuality progressively refines the VLM's perceptual capability. Extensive experiments show that EvoQuality boosts the base VLM's zero-shot performance by 31.8% on PLCC across diverse IQA benchmarks. Remarkably, despite being entirely self-supervised, EvoQuality achieves performance that is competitive with, or even surpasses, state-of-the-art supervised VLM-based IQA models, outperforming these models on 5 out of 7 IQA benchmarks. Furthermore, the framework demonstrates significant flexibility, allowing it to be stacked with pre-trained IQA models to bolster generalization on unseen datasets. Codes and checkpoints will be available at https://github.com/bytedance/EvoQuality.

12.
bioRxiv (Bioinfo) 2026-06-15

Multiple Fault Analysis and Drug Therapy on Signaling Pathways Using Dynamic Bayesian Network-based Model

Cell growth is an intricate biological phenomenon that is closely regulated by the interplay between various growth factors and transcription factors. Signaling pathways are the main mediators in this event, which provide the driving force for mitosis or sometimes meiosis. However, when malfunctions occur within the biological network, they can cause uncontrolled cell division, regardless of external stimuli. By employing Dynamic Bayesian Networks (DBNs), these malfunctions can be explicitly simulated, offering insights into their effects on cellular behavior and growth regulation. To a significant extent, the resultant outcomes can be mitigated through the use of reduced drug combinations. This study delves into the intricacies of signaling pathway behavior under the influence of concurrent malfunctions. Initially, we replicate the effects of these dysfunctions within DBNs. Subsequently, drug therapy is applied to alleviate their impact. Our methodology introduces a parameter known as efficiency_score, enabling the identification of optimized drug combinations without prior knowledge of specific dysfunctions. Particularly relevant in the context of realistic cancer conditions, these tailored drug inhibition points demonstrate enhanced efficacy compared to conventional treatments. Leveraging GPU acceleration throughout the modeling process accelerates the analysis of multiple faults within the biological networks, rendering our approach notably faster and more efficient.

13.
arXiv (CS.CV) 2026-06-12

Comparing Commercial Depth Sensor Accuracy for Medical Applications

Depth estimation has numerous medical and surgical applications. We benchmark four depth sensors on a porcine bone specimen, a porcine belly specimen, and a silicone kidney phantom using stylus-sampled references. These objects contain several real-world challenges, including homogeneous surfaces, specular surfaces, and subsurface scattering. The comparison includes stereo, structured-light, and time-of-flight sensors at a distance of approximately 50 cm. Specifically, the Intel RealSense D405 (Intel RealSense, United States), PMD Flexx2 (pmdtechnologies, Germany), Stereolabs ZED 2i (Stereolabs, France), and Zivid 2M+ 60 (Zivid, Norway) are compared. The Zivid 2M+ 60 performed best across all objects and metrics considered in this work. The ZED ranked second for real tissue, but last on the phantom.

14.
arXiv (CS.AI) 2026-06-11

Skill-Augmented AI Agents for Medical Research Analysis: An Exploratory Multi-Model Human Evaluation in an NSCLC Transcriptomic Biomarker Task

arXiv:2606.11830v1 Announce Type: new Abstract: Background. Large language models and AI agents are increasingly used to support biomedical research, but native model outputs may omit key analytical steps, misuse methods, or overstate conclusions. We evaluated whether autonomous access to a medical research skill package was associated with higher-quality AI-generated transcriptomic research-analysis outputs compared with native AI without skills. Methods. We conducted an exploratory multi-model human evaluation using a non-small cell lung cancer immunotherapy biomarker task. Six model backbones were tested. The evaluation included 21 anonymized outputs: 9 native-AI outputs and 12 skill-augmented outputs generated through an AI agent implementation represented by OpenClaw. Four non-expert biomedical reviewers and two blinded experts evaluated each output, with two ratings from each reviewer type. The primary outcome was expert-rated overall quality. Results. Skill-augmented outputs showed directionally higher expert overall quality than native-AI outputs (mean 5.50 vs 5.11; difference=0.39; bootstrap 95\% CI, -0.04 to 0.90; Welch p=0.156). Non-expert reviewer quality showed the same direction (mean 4.72 vs 4.47; difference=0.26; bootstrap 95\% CI, -0.25 to 0.80; Welch p=0.373). Expert agreement was limited (single-rating ICC=-0.15), and model-specific effects were descriptive and heterogeneous. Conclusions. Autonomous skill access showed a directional quality signal in this exploratory sample, but the signal was smaller than expert-rating noise and should not be interpreted as confirmatory evidence. The findings primarily motivate larger evaluations of skill-augmented AI agents with stronger reliability controls, platform replication, and biological-validity assessment.

15.
arXiv (CS.AI) 2026-06-11

HiGR: Industrial-Scale Hierarchical Generative Slate Recommendation Framework in Tencent

arXiv:2512.24787v4 Announce Type: replace-cross Abstract: Slate recommendation, which presents users with a ranked item list in a single display, is ubiquitous across mainstream online platforms. While recent generative recommendation methods have shown strong potential in modeling item sequences with semantic IDs, directly applying them to industrial-scale slate recommendation faces a fundamental disconnect: entangled SID spaces confound high-level list planning, fine-grained autoregressive decoding over long sequences limits semantic planning efficiency, and token-level objectives misalign with holistic slate quality. In this paper, we propose HiGR, an industrial-scale hierarchical generative framework for slate recommendation that bridges this disconnect through a co-designed pipeline. First, HiGR learns structured SIDs via a Prefix-Contrastive Residual Quantized VAE (PCRQ-VAE). By enforcing high-level prefixes to capture shared semantics, PCRQ-VAE creates a controllable discrete space that acts as a prerequisite for efficient planning. Leveraging this structured space, our Hierarchical Slate Decoder (HSD) shifts autoregressive modeling from entangled token-level decoding to coarse-grained preference embeddings. This design significantly reduces inference latency while allowing explicit global slate structure planning. Finally, this stable planning space enables an ORPO-based listwise alignment mechanism to optimize triple-objective implicit feedback-ranking fidelity, genuine user interest, and diversity. Extensive offline experiments show that HiGR outperforms state-of-the-art baselines by over 10% in offline recommendation quality while achieving a $5\times$ inference speedup. Online A/B tests on Tencent platforms further improve watch time by 1.22% and video plays by 1.73%. HiGR has been deployed on multiple Tencent platform surfaces, serving hundreds of millions of users and proving its industrial-scale applicability.

16.
arXiv (CS.AI) 2026-06-12

ReCal: Reward Calibration for RL-based LLM Routing

arXiv:2606.12479v1 Announce Type: cross Abstract: Large language model (LLM) routing has emerged as an effective paradigm for leveraging the complementary strengths of multiple LLMs through dynamic model and reasoning-strategy selection. Recent reinforcement learning (RL)-based routing methods further improve routing quality by optimizing routing policies from interaction feedback. However, they still struggle to provide informative and comparable learning signals under heterogeneous tasks with varying difficulty. In practice, multiple objectives (e.g., correctness, format behavior) are aggregated into a single scalar reward, leading to ambiguous credit assignment and conflicting optimization signals. Moreover, reward signals exhibit significant variability across instances, where some instances produce higher or more variable rewards, introducing optimization bias that favors trivial samples over informative ones. To address these issues, we propose ReCal, a \underline{Re}ward \underline{Cal}ibration framework for RL-based LLM routing. We first introduce a hierarchical reward decomposition mechanism with component-wise advantage estimation. We further propose a distribution-aware optimization strategy that calibrates optimization variability through variance-aware reweighting and per-dataset normalization. Experiments on seven datasets demonstrate that ReCal consistently improves routing performance, and training stability over baselines. Code is available at https://anonymous.4open.science/r/ReCal.

17.
arXiv (CS.AI) 2026-06-16

CoffeeBench: Benchmarking Long-Horizon LLM Agents in Heterogeneous Multi-Agent Economies

arXiv:2606.16613v1 Announce Type: new Abstract: As LLM agents become capable of increasingly long-horizon tasks, evaluating their performance in economic systems is becoming increasingly important. Unlike existing benchmarks that primarily evaluate a single agent interacting with a passive environment, economic systems are inherently multi-agent, requiring autonomous agents to communicate, negotiate, and transact while pursuing their own objectives over extended periods. We introduce CoffeeBench, a benchmark for evaluating LLM agents in a long-horizon multi-agent economy composed of heterogeneous firms. In CoffeeBench, two farmers, two roasters, and two retailers autonomously operate their businesses over a 90-day simulation, each seeking to maximize cumulative net income through communication and transactions while managing cash, inventory, and pricing. The evaluated model controls one coffee roaster, while the remaining firms are controlled by fixed reference agents. Across several recent open-weight and proprietary LLMs, all models outperform a passive baseline that takes no actions, with most achieving positive net income. Analysis of agent behavior reveals substantial differences in long-horizon economic interaction: higher-performing models communicate more actively with other firms, whereas Claude~Haiku~4.5 exhibits an idle-drift failure mode, repeatedly choosing inaction despite producing coherent assessments and plans. We release our code and agent trajectories to support future research.

18.
arXiv (CS.AI) 2026-06-18

NAVI-Orbital: First In-Orbit Demonstration of a Zero-Shot Vision-Language Model for Autonomous Earth Observation

arXiv:2606.18271v1 Announce Type: new Abstract: As Earth Observation data generation outpaces downlink bandwidth and human-in-the-loop processing, a widening gap has emerged between onboard collection and actionable ground intelligence. This paper presents NAVI-Orbital, a software system deployed on a Low Earth Orbit (LEO) spacecraft. On April 16, 2026, NAVI-Orbital achieved what is, to the authors' knowledge, the first in-orbit demonstration of a vision-language model performing autonomous multi-modal inference entirely onboard. NAVI-Orbital uses a local vision-language model (Gemma 3) to classify each captured scene, produce a text description of its content and the relationships between its features, and respond to operator follow-up via natural-language dialogue. The system is re-tasked through plain-English prompts in place of conventional command sequences, and is orchestrated by a graph-based state machine (LangGraph) coordinating dedicated agents for detection and dialogue. Results across ground benchmarking (88.16% accuracy on the 7,960-image curated AID benchmark), Flatsat validation, and live in-orbit captures of newly acquired, previously unseen Earth imagery (including uncorrected YAM-9 imagery, processed onboard with hardware-accelerated GPU inference and no fine-tuning for the flight instrument) demonstrate the feasibility of running foundation models on satellite-class edge computers to invert the conventional acquire-then-downlink-everything bandwidth profile through semantic compression of Earth observations in-orbit.

19.
arXiv (quant-ph) 2026-06-19

Entanglement structure of the dynamical phases in the sub-Ohmic spin-boson model

arXiv:2606.20313v1 Announce Type: new Abstract: The sub-Ohmic spin-boson model exhibits three distinct dynamical regimes in its spin population dynamics, classified as coherent, incoherent, and pseudo-coherent. Whether these regimes correspond to distinct spin-bath entanglement structures remains an open question. Here we address this using tree tensor network states with projector-splitting time evolution (TTN-TDVP-PS), scanning a broad grid in the sub-Ohmic $(s, \alpha)$ plane. We find that the spin entanglement entropy $S_\mathrm{spin}(t)$ reaches a stationary plateau on a timescale shorter than the polarization relaxation, enabling construction of a stationary entropy landscape from the stationary value $S_\mathrm{stable}$. Within this scalar entropy landscape, the entropy ridge broadly follows the population-based phase boundary at small $s$, but does not reproduce the two-branch structure at large $s$. The ridge remains single-valued within the incoherent region rather than separately tracking both population-based transitions. The Bloch-sphere representation provides a geometric interpretation of this behavior. The entropy plateau corresponds to trajectories settling onto constant-radius shells, with the ridge marking the parameters of smallest stationary Bloch radius. Mode-resolved bath entanglement shows that low-frequency modes dominate the environmental entropy scale and that coherent dynamics enhance bath-mode correlations beyond direct spin–mode correlations. These results establish the stationary spin entanglement entropy as a physically informative observable that complements population-based classifications of dissipative quantum dynamics.

20.
arXiv (math.PR) 2026-06-16

A tree-free approach to 3D Yang-Mills Langevin dynamic. Analytic estimates and the existence of a model for a regularity structure

arXiv:2605.14616v2 Announce Type: replace Abstract: Using the multi-index approach to regularity structures due to F. Otto et al., we construct a regularity structure and a model for it associated to the stochastic Langevin equation for the 3D Euclidean Yang-Mills functional. For the model we also obtain global stochastic and global pointwise weighted Besov type estimates which hold almost surely. The model is defined as a limit of a sequence of smooth models introduced with the help of a mollified noise. When the mollification is removed the sequence converges in a certain topology defined with the help of the stochastic estimates. To obtain these results we develop the multi-index approach for systems of equations with vector-valued white noises. This project is motivated by the problem for constructing 3D Euclidean Yang-Mills measure and by the earlier results of the author on the related problem of canonical quantization of the Yang-Mills field on the Minkowski space.

21.
arXiv (CS.AI) 2026-06-18

HeRo-Q: A General Framework for Stable Low Bit Quantization via Hessian Conditioning

arXiv:2601.21626v2 Announce Type: replace-cross Abstract: Post Training Quantization (PTQ), a mainstream model compression technique, often leads to the paradoxical 'low error, high loss' phenomenon because it focuses solely on minimizing quantization error. The root cause lies in the Hessian matrix of the LLM loss landscape: a few high curvature directions are extremely sensitive to perturbations. To address this, we propose the Hessian Robust Quantization (HeRo Q) algorithm, which applies a lightweight, learnable rotation-compression matrix to the weight space prior to quantization. This joint framework reshapes the loss landscape by reducing the largest Hessian eigenvalue and reducing its max eigenvalue, thereby significantly enhancing robustness to quantization noise. HeRo-Q requires no architectural modifications, incurs negligible computational overhead, and integrates seamlessly into existing PTQ pipelines. Experiments on Llama and Qwen models show that HeRo Q consistently outperforms state of the art methods including GPTQ, AWQ, and SpinQuant not only achieving superior performance under standard W4A8 settings, but also excelling in the highly challenging W3A16 ultra low bit regime, where it boosts GSM8K accuracy on Llama3 8B to 70.15\% and effectively avoids the logical collapse commonly seen in aggressive quantization.

22.
arXiv (CS.LG) 2026-06-12

The Metric Picks the Winner: Evaluation Choice Flips Model Rankings for Drug-Response Prediction in Unseen Chemistry

arXiv:2606.12639v1 Announce Type: new Abstract: Predicting how a cell's transcriptome responds to a drug it has never seen is a core, hard problem in computational cell biology: recent benchmarks show complex models often fail to beat trivial baselines once test compounds are held out by chemistry. We study one cell line and assay, THP-1 cells profiled by DRUG-seq, scored by the active-compound weighted MSE(wMSE) of the VCPI prediction contest. We propose a staged approach: dumb baselines (untreated control and mean training-compound response) that the field keeps failing to beat; non-parametric retrieval (a Tanimoto-weighted average of a held-out compound's nearest training compounds); and a fusion stage combining a frozen chemistry embedding with retrieval-support features to predict the residual over the mean, with an uncertainty head and gene programs. On the released VCPI THP-1 drug-seq data (14,026 training compounds), under a Bemis-Murcko scaffold split, the model ranking inverts depending on the metric. Under an inverse-variance per-gene proxy, a regularized linear regression on Morgan fingerprints appears to win over the deep models, retrieval, and ChemBERTa – the textbook "simple baselines win" result. But under the contest's true active-set metric (per-(gene, compound) Mejia weights, validated against the official scorer; mean baseline 0.535 vs the organizers' 0.507 reference), that reverses: the deep models win, our fusion decoder significantly beats the linear fingerprint baseline (-0.012 wMSE, paired bootstrap p < 10^-4), and the proxy's winner becomes the worst chemistry-aware predictor. Picking the metric picks the winner – to our knowledge the first demonstration on real held-out drug chemistry of the metric-calibration effect established largely on genetic perturbation. We release a reproducible pipeline wired to the official scorer that emits a valid submission over the real 1064 x 12,995 grid.

23.
arXiv (CS.LG) 2026-06-12

Physics-Aware Auxiliary Losses Improve Out-of-Distribution Generalization of a GNN Synthesizability Filter

arXiv:2606.12651v1 Announce Type: new Abstract: Machine-learning drug-discovery pipelines increasingly rely on generative models that propose molecules far from the data used to train downstream synthesizability filters. Existing filters (SAScore, SCScore, RAscore, DeepSA) are purely statistical and degrade in exactly this out-of-distribution (OOD) regime. We ask whether cheap, closed-form physical priors, used as auxiliary supervision on a graph neural network (GNN), improve OOD generalization. We add two auxiliary losses to a GINE backbone: a topological complexity regression supervised by the Bertz index, and a strain-energy soft penalty supervised by MMFF94 force-field energy. On a 65,177-molecule corpus (HIV, Tox21, COCONUT) labeled by SAScore thresholds we reproduce a strong in-distribution baseline, then evaluate a 4-way ablation (baseline / +complexity / +strain / +both) on a single-source OOD split (train on drug-like HIV+Tox21, test on COCONUT natural products), repeated over 5 seeds with paired bootstrap confidence intervals. All three physics-aware variants give a small but statistically significant OOD improvement over the baseline (mean OOD AUC 0.9774): +complexity Delta = +0.0060 (95% CI [+0.0023, +0.0102]), +strain Delta = +0.0032 ([+0.0008, +0.0052]), +both Delta = +0.0066 ([+0.0038, +0.0093]); every interval excludes zero, and the combination is best. The variants are indistinguishable in-distribution, so the effect is visible only under OOD evaluation. We are explicit that the effects are modest, and we report a cautionary methodological finding: a single-seed version of this experiment produced a qualitatively different (non-monotone) story that did not survive multi-seed evaluation.

24.
arXiv (quant-ph) 2026-06-17

Cavity method for permutation models on Cayley trees

arXiv:2606.17751v1 Announce Type: new Abstract: Motivated by permutation statistical models arising in random tensor networks, we study permutation models on a Cayley tree whose variables take values in the symmetric group $\Sn$. The pair interaction is assumed to depend only on the cycle type of the relative permutation. Then the Boltzmann weight is written as a class function on $\Sn$. This property diagonalizes the edge convolution operator in irreducible representation sectors. As a result, the linear stability of the uniform paramagnetic cavity solution is controlled by the character eigenvalue ratios. For cycle-factorized weights, these eigenvalues can be expressed as specializations of Schur functions. We derive the instability criteria and also verify their validity by comparison with direct numerical iterations of the cavity equation.

25.
arXiv (CS.CL) 2026-06-12

SICI: A Semantic-Pragmatic Complexity Index Reveals Regime Shifts in LLM Stance Detection

Prompt-based LLMs are increasingly used for stance detection, but harder examples are not always repaired by clearer instructions, reasoning prompts, retrieval, or debate. We introduce SICI (Stance Inference Complexity Index), a seven-dimensional diagnostic measure of the semantic-pragmatic burden imposed by a target–text pair. Across SemEval-2016 and VAST, SICI predicts LLM accuracy better than surface proxies and shows substantial cross-scorer reliability ($\alpha=0.771$). More importantly, LLM errors change regime as SICI increases: low-complexity examples invite over-attribution, especially Against predictions; intermediate examples form an unstable boundary; and high-complexity examples rapidly concentrate on None. This phase-transition-like structure persists across GPT-3.5, GPT-4o-mini, DeepSeek-V3, and GPT-4o, although stronger models move the boundaries. A 15-method intervention study further shows that prompting, retrieval, and debate often shift models along the attribution–abstention axis rather than removing the high-complexity bottleneck.